6FUP

F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PACT Premier E08: 0.2 M Na SO4, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5150.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.28α = 90
b = 115.16β = 90
c = 50.71γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2012-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7246.4198.60.0410.045123.66.653476
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.7799.40.7410.8020.8142.76.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6EH61.7246.4150709271599.380.178020.176130.21484RANDOM33.454
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.370.9-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.238
r_dihedral_angle_4_deg14.708
r_dihedral_angle_3_deg13.824
r_dihedral_angle_1_deg7.726
r_long_range_B_other6.423
r_long_range_B_refined6.422
r_scangle_other2.826
r_mcangle_it2.154
r_mcangle_other2.154
r_scbond_it1.942
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.238
r_dihedral_angle_4_deg14.708
r_dihedral_angle_3_deg13.824
r_dihedral_angle_1_deg7.726
r_long_range_B_other6.423
r_long_range_B_refined6.422
r_scangle_other2.826
r_mcangle_it2.154
r_mcangle_other2.154
r_scbond_it1.942
r_scbond_other1.932
r_angle_refined_deg1.847
r_mcbond_it1.366
r_mcbond_other1.358
r_angle_other_deg1.048
r_chiral_restr0.116
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3493
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
PHASERphasing